Lab 5b

library("tidyverse")

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## ✓ ggplot2 3.3.2     ✓ purrr   0.3.4
## ✓ tibble  3.0.3     ✓ dplyr   1.0.2
## ✓ tidyr   1.1.2     ✓ stringr 1.4.0
## ✓ readr   1.3.1     ✓ forcats 0.5.0

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library("lubridate")

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library("ggthemes")

Read data & format

# Read time series data for confirmed cases & switch to long
time_series_confirmed_long <- read_csv(url("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv")) %>%
  rename(Province_State = "Province/State", Country_Region = "Country/Region")  %>% 
               pivot_longer(-c(Province_State, Country_Region, Lat, Long),
                             names_to = "Date", values_to = "Confirmed") 

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##   .default = col_double(),
##   `Province/State` = col_character(),
##   `Country/Region` = col_character()
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# Read time series data for deaths & switch to long
time_series_deaths_long <- read_csv(url("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")) %>%
  rename(Province_State = "Province/State", Country_Region = "Country/Region")  %>% 
  pivot_longer(-c(Province_State, Country_Region, Lat, Long),
               names_to = "Date", values_to = "Deaths")

## Parsed with column specification:
## cols(
##   .default = col_double(),
##   `Province/State` = col_character(),
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## )

## See spec(...) for full column specifications.

# Make keys for both tables 
time_series_confirmed_long <- time_series_confirmed_long %>% 
  unite(Key, Province_State, Country_Region, Date, sep = ".", remove = FALSE)
time_series_deaths_long <- time_series_deaths_long %>% 
  unite(Key, Province_State, Country_Region, Date, sep = ".") %>% 
  select(Key, Deaths)

# Join tables
time_series_long_joined <- full_join(time_series_confirmed_long,
    time_series_deaths_long, by = c("Key")) %>% 
    select(-Key)

# Reformat dates
time_series_long_joined$Date <- mdy(time_series_long_joined$Date)

# Create report table with counts
time_series_long_joined_counts <- time_series_long_joined %>% 
  pivot_longer(-c(Province_State, Country_Region, Lat, Long, Date),
               names_to = "Report_Type", values_to = "Counts")

Graphic Output

# Plot graph to pdf outputfile 
pdf("Graphs/time_series_example_plot.pdf", width = 6, height = 3)
time_series_long_joined %>% 
  group_by(Country_Region, Date) %>% 
  summarise_at(c("Confirmed", "Deaths"), sum) %>% 
  filter(Country_Region == "US") %>% 
  ggplot(aes(x = Date, y = Deaths)) +
  geom_point() +
  geom_line() +
  ggtitle("US COVID-19 Deaths")
dev.off()

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# Plot graph to png outputfile
ppi <- 300
png("Graphs/time_series_example_plot.png", width=6*ppi, height=6*ppi, res=ppi)
time_series_long_joined %>% 
  group_by(Country_Region,Date) %>% 
  summarise_at(c("Confirmed", "Deaths"), sum) %>% 
  filter (Country_Region == "US") %>% 
    ggplot(aes(x = Date,  y = Deaths)) + 
    geom_point() +
    geom_line() +
    ggtitle("US COVID-19 Deaths")
dev.off()

## quartz_off_screen 
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RMarkdown loading images

# Load image into RMarkdown file using pngs

US COVID-19 Deaths

Interactive graphs

library(plotly)

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ggplotly(
  time_series_long_joined %>% 
    group_by(Country_Region,Date) %>% 
    summarise_at(c("Confirmed", "Deaths"), sum) %>% 
    filter (Country_Region == "US") %>% 
    ggplot(aes(x = Date,  y = Deaths)) + 
      geom_point() +
      geom_line() +
      ggtitle("US COVID-19 Deaths") +
    theme_clean())

Animated graphs

library("gganimate")
library("transformr")
library("gifski")
theme_set(theme_clean())

data_time <- time_series_long_joined %>% 
    group_by(Country_Region,Date) %>% 
    summarise_at(c("Confirmed", "Deaths"), sum) %>% 
    filter (Country_Region %in% c("China","Korea, South","Japan","Italy","US")) 
p <- ggplot(data_time, aes(x = Date,  y = Confirmed, color = Country_Region)) + 
      geom_point() +
      geom_line() +
      ggtitle("Confirmed COVID-19 Cases") +
      geom_point(aes(group = seq_along(Date))) +
      transition_reveal(Date) 
# Some people needed to use this line instead
animate(p,renderer = gifski_renderer(), end_pause = 15)